RI predictions

[Qiong-Yang]

I want to use your model to make some predictions about molecular RI, but I always run into the following problems: -- Attaching packages -------------------------------------------------------------------------------------------------------------------------- tidyverse 1.3.0 -- √ ggplot2 3.3.2 √ purrr 0.3.4 √ tibble 3.0.4 √ dplyr 1.0.2 √ tidyr 1.1.2 √ stringr 1.4.0 √ readr 1.4.0 √ forcats 0.5.0 -- Conflicts ----------------------------------------------------------------------------------------------------------------------------- tidyverse_conflicts() -- x dplyr::filter() masks stats::filter() x dplyr::lag() masks stats::lag() Use suppressPackageStartupMessages() to eliminate package startup messages.

Attaching package: ‘shinyjs’

The following object is masked from ‘package:shiny’:

runExample

The following objects are masked from ‘package:methods’:

removeClass, show

Attaching package: ‘ChemmineR’

The following object is masked from ‘package:dplyr’:

groups

The following object is masked from ‘package:tibble’:

view

Listening on http://127.0.0.1:4163 Warning: Error in py_call_impl: AttributeError: 'str' object has no attribute 'decode' 82:

So hopefully you can help me get the molecular RIs predictions

[TomasVrzal]

What version of h5py do you use? Maybe downgrading the h5py could be helpful.

[Qiong-Yang]

thanks, now i get new problem like this:

library(ChemmineR) library(ChemmineOB) library(keras) library(tensorflow) library(reticulate) library(DeepReI)

DeepReI()

Listening on http://127.0.0.1:4885 Warning in readLines(file, ...) : 读'C:\Users\15362\AppData\Local\Temp\RtmpcFWnJc/08eed10b2e2fcfd1cb456019/0.txt'时最后一行未遂 Warning: Error in getClass: “_p_std__string” is not a defined class [No stack trace available]

[TomasVrzal]

What version of Chemminer and ChemmineOB do you have?

[Qiong-Yang]

ChemmineOB_1.28.0 ChemmineR_3.41.2

sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936 LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C LC_TIME=Chinese (Simplified)_China.936

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] ChemmineOB_1.28.0 writexl_1.3.1 ChemmineR_3.41.2 shinyjs_2.0.0 shinybusy_0.2.2 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4 readr_1.4.0
[11] tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.3 tidyverse_1.3.0 shiny_1.5.0 DeepReI_0.1.0 reticulate_1.18 tensorflow_2.2.0.9000 keras_2.3.0.0

loaded via a namespace (and not attached): [1] bitops_1.0-6 fs_1.5.0 usethis_2.0.0 lubridate_1.7.9.2 devtools_2.3.2 httr_1.4.2 rprojroot_2.0.2 tools_4.0.3 backports_1.2.1 DT_0.17 R6_2.5.0
[12] DBI_1.1.0 colorspace_2.0-0 withr_2.3.0 gridExtra_2.3 tidyselect_1.1.0 prettyunits_1.1.1 processx_3.4.5 compiler_4.0.3 cli_2.2.0 rvest_0.3.6 xml2_1.3.2
[23] desc_1.2.0 scales_1.1.1 callr_3.5.1 rappdirs_0.3.1 tfruns_1.4 digest_0.6.27 base64enc_0.1-3 pkgconfig_2.0.3 htmltools_0.5.0 sessioninfo_1.1.1 dbplyr_2.0.0
[34] fastmap_1.0.1 htmlwidgets_1.5.3 rlang_0.4.10 readxl_1.3.1 rstudioapi_0.13 generics_0.1.0 jsonlite_1.7.2 RCurl_1.98-1.2 magrittr_2.0.1 Matrix_1.2-18 Rcpp_1.0.5
[45] munsell_0.5.0 fansi_0.4.1 lifecycle_0.2.0 stringi_1.5.3 whisker_0.4 zlibbioc_1.36.0 pkgbuild_1.2.0 grid_4.0.3 promises_1.1.1 crayon_1.3.4 lattice_0.20-41
[56] haven_2.3.1 hms_0.5.3 zeallot_0.1.0 ps_1.5.0 pillar_1.4.7 rjson_0.2.20 pkgload_1.1.0 reprex_0.3.0 glue_1.4.2 remotes_2.2.0 BiocManager_1.30.10 [67] modelr_0.1.8 png_0.1-7 vctrs_0.3.6 httpuv_1.5.4 testthat_3.0.1 cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1 xfun_0.20 mime_0.9 xtable_1.8-4
[78] broom_0.7.3 rsvg_2.1 later_1.1.0.1 tinytex_0.28 memoise_1.1.0 ellipsis_0.3.1

[TomasVrzal]

Please try the following code:

library(ChemmineR) data(sdfsample) propOB(sdfsample)

Everything went well or some error appeared?

[Qiong-Yang]

when i run the code: library(ChemmineR) data(sdfsample) propOB(sdfsample)

error like this :

library(ChemmineR) data(sdfsample) propOB(sdfsample) Error in getClass(Class, where = topenv(parent.frame())) : “_p_std__string” is not a defined class

library(ChemmineOB) molRefs = forEachMol("SMILES","C1CCCCC1\ttest-compound-name",identity) prop_OB(molRefs) Error in getClass(Class, where = topenv(parent.frame())) : “_p_std__string” is not a defined class

library(DeepReI) DeepReI()

Listening on http://127.0.0.1:3489 Warning in readLines(file, ...) : 读'C:\Users\15362\AppData\Local\Temp\RtmpS6Wczm/a4e687851de9844a5c09d99e/0.txt'时最后一行未遂 Warning: Error in getClass: “_p_std__string” is not a defined class [No stack trace available]

[TomasVrzal]

The problem is in ChemmineR (see https://support.bioconductor.org/p/p133478/) Probably ChemmineR downgrading would work.